Surveillance for COVID-19 Using Wastewater and Advancing Nasal Self-Collection of Specimens (SWANSS) in an Atlanta Jail Open Access
Saber, Lindsay (Spring 2022)
Abstract
Background: Correctional facilities historically house some of the most vulnerable persons in our society. With crowded living conditions, decreased access to quality medical care, and limited resources, infectious disease outbreaks can be extremely dangerous, particularly for highly transmissible diseases like COVID-19. Wastewater-Based Surveillance is a low- cost, highly sensitive, non- invasive method that can provide an early warning of COVID-19 surges in the community and outbreaks in institutions, but this has not yet been applied in correctional facilities.
Objective: The study’s main objective was to examine if WBS is a practical and sensitive strategy to surveil for new COVID-19 outbreaks in a large jail setting.
Methods: The study period was from June 15, 2021 to March 16, 2022 (39 weeks). COVID-19 diagnostic tests were administered to jail residents and analyzed on a weekly basis—rapid diagnostic test data was collected daily by the jail administration, and 16 mass PCR testing events were conducted by the study team. Wastewater samples were collected via Moore swabs on 28 unique weeks and analyzed for SARS-CoV-2 by realtime RT-qPCR. Temporal and correlation analysis were applied to wastewater and COVID-19 diagnostic test results to examine the association between the prevalence of COVID-19 identified by diagnostic testing and detection of SARS-CoV-2 RNA in the wastewater.
Results: The efficiency of diagnostic testing increased with repeated trials and improved staffing. During the study period, COVID-19 test positivity ranged from 0% to 29.5%. SARS-CoV-2 RNA was detected in the wastewater samples from 25 of the 28 weeks with samples. Wastewater collection and analysis was feasible for a team with a designated sampling and lab team. Stronger RT-PCR signals for SARS-CoV-2 in the jail wastewater preceded rises in the number of COVID-19 cases in the jail, and regression analysis indicated a strong relationship between SARS-CoV-2 RNA concentrations in wastewater samples and positivity rates of COVID-19 diagnostic testing.
Conclusions SARS-CoV-2 RNA detection in wastewater collected at the jail was associated with COVID-19 diagnostic test results in the jail population. Wastewater based surveillance is a practical strategy to surveil for new COVID-19 outbreaks in a jail setting.
Table of Contents
Chapter 1:
Introduction_________________________________________________________________________________1
Chapter 2:
Literature Review___________________________________________________________________________ 3
COVID-19 in United States Correctional Facilities_______________________________________3
Infectious Diseases in Correctional Facilities____________________________________________4
COVID-19 in Correctional Facilities______________________________________________________6
COVID-19 Diagnostics Methods__________________________________________________________7
COVID-19 Diagnostics in Jails____________________________________________________________8
Wastewater Based Surveillance for COVID-19 ___________________________________________9
Overview____________________________________________________________________________9
Wastewater Based Surveillance Methods___________________________________________9
Previous Studies on Wastewater Surveillance ____________________________________12
Fecal Shedding Characteristics____________________________________________________12
Wastewater Surveillance at Institutions___________________________________________13
Wastewater Based Surveillance in a Jail__________________________________________________15
Chapter 3:
Introduction_________________________________________________________________________________16
Research Objective__________________________________________________________________________18
Rationale____________________________________________________________________________________18
Methods_____________________________________________________________________________________19
COVID-19 Diagnostic testing_____________________________________________________________19
PCR Nasal Swab Collection_________________________________________________________19
_ RT-PCR Test Procedure____________________________________________________________________20
Rapid Test Collection_______________________________________________________________21
Wastewater Based Surveillance___________________________________________________________22
Sample Collection__________________________________________________________________22
Laboratory Analysis________________________________________________________________23
Interpreting Results_______________________________________________________________23
Data Analysis______________________________________________________________________________25
COVID-19 Diagnostic Testing Analysis_____________________________________________25
Wastewater Data Analysis___________________________________________________________26
Results________________________________________________________________________________________27
COVID-19 Diagnostic Testing_____________________________________________________________28
Wastewater Testing Results_______________________________________________________________33
Relationship between Diagnostic Test Results and Wastewater Monitoring Results____35
Discussion____________________________________________________________________________________41
Mass COVID-19 Diagnostic Testing in a Jail______________________________________________41
WBS Testing in a Jail_______________________________________________________________________44
Using WBS to predict individual diagnostic cases________________________________________46
Strengths____________________________________________________________________________________ 48
Limitations__________________________________________________________________________________ 48
Conclusion__________________________________________________________________________________ 50
Chapter 4:
Recommendations__________________________________________________________________________ 51
References___________________________________________________________________________________52
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